As long as we do not know exactly how you created those midi's one can not say or conclude much, except there are duplicates or overlaps. But why, because of what is still unknown, because the entire process in unknown.
If you want to analyze this in detail you should check after each editing/recording step what is changing where? Having external midi files would allow using external command line midi tools for cleaning up duplicates, for example, or anything else you would need. Apart from the million features inside Reaper, with or without scripts. Good luck with your project.
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